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Structure of YcfC Protein of Unknown Function Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other MIRAS model built by WARP/ARP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, zinc acetate, lithium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.102 α = 90 b = 62.749 β = 90 c = 68.399 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD CUSTOM-MADE 2003-08-24 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD CUSTOM-MADE 2003-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.999871 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 19-ID 0.91963 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2 1.95 50 82.6 0.107 15.87 13895 11477 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 1.98 36.7 0.423 1.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MIRAS Build by WARP/ARP 2 25 11138 11138 85.24 0.15729 0.15729 0.164 16.821
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.99 0.8 0.19
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 11.153 r_scangle_it 9.392 r_scbond_it 7.548 r_mcangle_it 6.47 r_mcbond_it 5.321 r_dihedral_angle_1_deg 5.268 r_angle_refined_deg 1.582 r_angle_other_deg 0.911 r_metal_ion_refined 0.367 r_symmetry_vdw_other 0.269
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 11.153 r_scangle_it 9.392 r_scbond_it 7.548 r_mcangle_it 6.47 r_mcbond_it 5.321 r_dihedral_angle_1_deg 5.268 r_angle_refined_deg 1.582 r_angle_other_deg 0.911 r_metal_ion_refined 0.367 r_symmetry_vdw_other 0.269 r_nbd_other 0.231 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.22 r_symmetry_vdw_refined 0.154 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.091 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1605 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing